/*
 * Copyright (c) 2011 Seoul National University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met: redistributions of source code must retain the above copyright
 * notice, this list of conditions and the following disclaimer;
 * redistributions in binary form must reproduce the above copyright
 * notice, this list of conditions and the following disclaimer in the
 * documentation and/or other materials provided with the distribution;
 * neither the name of the copyright holders nor the names of its
 * contributors may be used to endorse or promote products derived from
 * this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * Authors: Jung Ho Ahn  ( gajh@snu.ac.kr )
 *
 */

#include <fstream>
#include <cstring>
#include "FastAReader.h"


int FastAReader::readToBuffer(SequenceBuffer * seqbuf) {
	static bool firstread = false;
	//char buf[seqbuf->getMaxLength()];
	char buf[2048];
	//char linebuf[seqbuf->getMaxLength()];
    char linebuf[2048];
	int cnt = 0;

	// strip first line and check it is really fasta format
	if(firstread == false) {
		firstread = true;
		infile.getline(linebuf, sizeof(linebuf));
		if(linebuf[0] != '>') {
			// seems not fastq file...
			return -1;
		}
	}

	while(infile.good() && seqbuf->hasMoreSpace()) {
		buf[0] = '\0';
		while(infile.getline(linebuf, sizeof(linebuf))) {
			if(linebuf[0] == '>') break;
			strcat(buf, linebuf);
		}
		seqbuf->addLine(buf);
		cnt++;
	}
	return cnt;
}
